This paper presents a systematic investigation that encompasses the safety assessment of a fuel preparation room (FPR) intended for a hydrogen-fueled ship. The primary objective is to determine the appropriate ventilation strategy to mitigate the risks associated with potential hydrogen leakage. The study focuses on a case involving an FPR measuring 10.2 m × 5.3 m × 2.65 m, which is part of a 750 DWT hydrogen-powered fishing vessel. To identify the potential events leading to hydrogen dispersion, an event tree analysis is conducted. Additionally, existing regulations and guidelines related to the safety assessments of hydrogen leakage in enclosed areas are summarized and analyzed. Computational fluid dynamics, FLACS-CFD, are utilized for the consequence analysis in order to evaluate the impact of ventilation on hydrogen dispersion and concentration within the FPR. The research findings indicate significant effects of ventilation on the hazards and safety assessments of FPRs and high-pressure fuel gas supply systems. The study highlights that hydrogen vapor tends to accumulate at the ceiling and in the corners and spaces created by the equipment. The position and size of ventilation openings greatly influence the dispersion of hydrogen leakage. Proper ventilation design, including top inlet ventilation and outlet ventilation on the opposite side, helps to maintain a safe FPR by facilitating the efficient dispersion of hydrogen vapor. Moreover, locating inlet ventilation on the same side as the outlet ventilation is found to hinder dispersion, while the cross-ventilation achieved by placing inlets and outlets on opposite sides enhances airflow and dispersion. Consequently, it is recommended to prioritize the structural design of FPRs and implement enhanced safety measures. Additionally, updating the relevant regulations to address these concerns is strongly advised.